Sanghyun Park and Klaus Schulten.
Calculating potentials of mean force from steered molecular dynamics
simulations.
Journal of Chemical Physics, 120:5946-5961, 2004.
PARK2004
Steered molecular dynamics (SMD) permits efficient investigations of
molecular processes by focusing on selected degrees of freedom. We
explain how one can, in the framework of SMD, employ Jarzynski's
equality (also known as the nonequilibrium work relation) to calculate
potentials of mean force (PMF). We outline the theory that serves
this purpose and connects nonequilibrium processes (such as SMD
simulations) with equilibrium properties (such as the PMF). We review
the derivation of Jarzynski's equality, generalize it to isobaric-isothermal
processes, and discuss its implications in relation to the second law of
thermodynamics and computer simulations. In the relevant regime of
steering by means of stiff springs, we demonstrate that the work on the
system is Gaussian-distributed regardless of the speed of the process
simulated. In this case, the cumulant expansion of Jarzynski's equality
can be safely terminated at second order. We illustrate the PMF
calculation method for an exemplary simulation and demonstrate the
Gaussian nature of the resulting work distribution.
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